Read Me

Installing and using COCO:

- uncompress the package in a location of your choice
- start Matlab
- in Matlab change to coco/toolboxes
- execute startup.m

COCO is now ready to be used.

The documentation for the tutorial examples of the book "Recipes for 
continuation" is still under development. The entry page can be opened with 
"doc Recipes" (note the capital R). Unfortunately, Matlab has no concept of 
distinguishing help text for several versions of the same toolbox. At the 
moment one can see the documentation for the tutorial toolboxes that are 
either first on the path or are in the current directory. We are working on 
fixing this problem.




The text below is largely outdated. An up-to-date reference is found in the 
book

	Recipes for Continuation
	Harry Dankowicz and Frank Schilder
	http://www.ec-securehost.com/SIAM/CS11.html


########################################################################
The statements below are somewhat outdated. Please read the short reference 
in doc/ShortReference for an introduction. Theoretical background about the 
implementation can be found in:

H. Dankowicz, F. Schilder; An extended continuation problem for bifurcation 
analysis in the presence of constraints, ASME Journal of Computational and 
Nonlinear Dynamics, Vol. 6, No. 3, 031003, 2011.


Using COCO:

- uncompress the package
- start Matlab
- in Matlab change to coco/toolboxes
- execute startup.m
- change to coco/examples and run the demos

To simplify using coco you might want to execute startup.m whenever Matlab 
starts. Please see the Matlab documentation for how to do this.

The text below is outdated. There will soon be a paper on the mathematical 
concepts of the core and we will update the documentation in the M-files of 
coco.

#####################################################################
This file contains some very basic documentation of ideas fundamental to this 
package. The ultimate source of reference is still the source code though.



1. The philosophy of the data structure opts
--------------------------------------------

The basic objectives behind the opts structure are to make it easy to replace 
parts of an algorithm, to avoid the use of global variables or long argument 
lists and to store the full state of the continuation algorithm in an 
organised way. For example, it should be possible to replace Newton's method 
with another algorithm, or the code for 1D continuation with a code for 2D 
continuation. Also, the user should be able to set certain constants 
influencing algorithms in a fairly simple way.

The dependencies within individual parts of a continuation code have the form 
of a graph. This graph may be quite deep and may contain loops (it is not a 
tree). We represent such a graph as a dictionary, that is, a table with two 
columns, a class name and a set of values. This table is encoded as a 
structure and the principal form of access is

  val = opts.class_name.property_name

Now, a class like 'cont' may contain a property named 'corrector', which 
specifies the corrector to use by the continuation method. It would access 
functions and properties defined by this corrector with

  corrector = opts.cont.corrector
  opts = opts.(corrector).some_function(opts, ...)

This is similar to pointers and one can exchange the corrector by assigning a 
non-default value to the property 'corrector' of the class 'cont'. This way 
it is possible to represent arbitrary graphs with a flat data structure.

You should aim at making it possible to replace algorithms in a transparent 
way as much as possible. You should pass and return the opts structure 
in/from any algorithm. Use function definitions like

  function [opts, varargout] = some_function(opts, varargin)

This somewhat strange syntax of having an input and output argument with the 
same name allows Matlab to optimise access to the structure opts (that is, to 
avoid any unnecessary copying).



2. The concept of sub-toolboxing
--------------------------------

The idea of sub-toolboxing is to make it possible that any toolbox for some 
continuation problem can be used as a building block for other toolboxes. 
Take, as a simple example, the continuation of homoclinic orbits. The classic 
way to attack this problem is to construct a BVP that contains the equations 
for the fixed point and its invariant manifolds in the boundary conditions. A 
more natural way seems to be to combine two toolboxes, one for fixed point 
continuation with another one for solutions of boundary value problems. These 
two toolboxes would become sub-toolboxes of a homoclinic orbit toolbox, which 
in turn is a sub-toolbox for the continuation code.

Toolboxes like MPBVP should be designed keeping this in mind. They should 
provide a full set of interface functions for constructing and manipulating 
equations and for accessing all parts of the solution in a well-defined way.

The ideal toolbox does a specific well-defined job and can be replaced by any 
other toolbox offereing the same interface.

At the moment our toolboxes do not strictly follow this idea as the entry 
functions with names defined as

  func_name = sprintf('%s_%s2%s', TOOLBOX, FROM_ST, TO_ST)

call Newton's method COCO explicitly. Instead, they should only construct an 
algorithm in functional form and an initial solution and then return to COCO. 
This will be one of the more important changes to this package; see the next 
section for more details.



3. Changes planned in the future
--------------------------------

There are several changes we want to make, which are due to design 
limitations that we discovered during testing.

We plan to reorganise the finite state machine for the continuation code. The 
main goal is to split it properly according to functionality. The corrector 
is already a separate toolbox. Similarly, we will have a rather abstract 
continuation code and a toolbox representing a manifold. The latter toolbox 
will become responsible for constructing an apropriate data structure, the 
construction of extended systems, the prediction and mesh-adaptation (of the 
mesh of the family of solutions, not the collocation points). The 
continuation code will be rearranged to work with srbitrary-dimensional 
families of solutions.

Another major addition is to enable additional constraints and test 
functions. This is quite complicated and may strongly influence the 
communication with other toolboxes. As yet it is not clear how we are going 
to implement this important feature. We aim at making it possible to add 
constraints and allow the continuation of higher co-dimension 
curves/families. We also aim at making this independent of the dimension of 
the family of solutions.

There are a number of other changes that may influence other toolboxes. 
Please see the file toolbox/todo.txt for a complete list of open problems.